Bisi Ojediran, Shell's spokesperson, said the flow station had been shut down as a precaution, cutting production by 12,000 barrels of oil per day.
The group called itself the Niger Delta Freedom Fighters, Shell's Ojediran said.
He did not say if the previously unheard-of group had made any specific demands.
Attacks on pipelines and oil facilities have cut the West African country's usual daily output of 2.5 million barrels by about a quarter this year.
Scores of oil workers - most of them Nigerians - typically live in such compounds. Ojediran declined to say how many people had been in the facility.
Attacks have become common in the southern river delta of Africa's largest crude producer.
Attackers have ranged from armed forces saying they're fighting for the freedom of their imprisoned leaders and a greater share of oil wealth to criminal gangs looking for a quick ransom from hostages.
Benemesia - head of a government-funded group that is attempting to curb attacks in Bayelsa - said he had not seen the assault himself, but had talked to members of his group at the scene.
Nigeria is the fifth-largest supplier of oil to the United States, and attacks in the Niger river delta have often moved world oil markets.
This latest incident occurred as the oil-exporting cartel Opec wrapped up a meeting in Nigeria's far-off capital, Abuja.
On Thursday, the group said it planned to cut its output in early 2007, pushing oil prices above $62 a barrel.